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Tan J, Xu Y, Wang X, Yan F, Xian W, Liu X, Chen Y, Zhu Y, Zhou Y. Molecular basis of threonine ADP-ribosylation of ubiquitin by bacterial ARTs. Nat Chem Biol 2024; 20:463-472. [PMID: 37945894 DOI: 10.1038/s41589-023-01475-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 10/08/2023] [Indexed: 11/12/2023]
Abstract
Ubiquitination plays essential roles in eukaryotic cellular processes. The effector protein CteC from Chromobacterium violaceum blocks host ubiquitination by mono-ADP-ribosylation of ubiquitin (Ub) at residue T66. However, the structural basis for this modification is unknown. Here we report three crystal structures of CteC in complexes with Ub, NAD+ or ADP-ribosylated Ub, which represent different catalytic states of CteC in the modification. CteC adopts a special 'D-E' catalytic motif for catalysis and binds NAD+ in a half-ligand binding mode. The specific recognition of Ub by CteC is determined by a relatively separate Ub-targeting domain and a long loop L6, not the classic ADP-ribosylating turn-turn loop. Structural analyses with biochemical results reveal that CteC represents a large family of poly (ADP-ribose) polymerase (PARP)-like ADP-ribosyltransferases, which harbors chimeric features from the R-S-E and H-Y-E classes of ADP-ribosyltransferases. The family of CteC-like ADP-ribosyltransferases has a common 'D-E' catalytic consensus and exists extensively in bacteria and eukaryotic microorganisms.
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Affiliation(s)
- Jiaxing Tan
- The MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Department of Gastroenterology of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yan Xu
- The MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xiaofei Wang
- The MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Department of Gastroenterology of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Fujie Yan
- The MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Wei Xian
- Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Xiaoyun Liu
- Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Yan Chen
- Department of Gastroenterology of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yongqun Zhu
- The MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Department of Gastroenterology of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yan Zhou
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, China.
- Department of Infectious Diseases, Sir Run Run Shaw Hospital School of Medicine, Zhejiang University, Hangzhou, China.
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2
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Papatheodorou P, Minton NP, Aktories K, Barth H. An Updated View on the Cellular Uptake and Mode-of-Action of Clostridioides difficile Toxins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1435:219-247. [PMID: 38175478 DOI: 10.1007/978-3-031-42108-2_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Research on the human gut pathogen Clostridioides (C.) difficile and its toxins continues to attract much attention as a consequence of the threat to human health posed by hypervirulent strains. Toxin A (TcdA) and Toxin B (TcdB) are the two major virulence determinants of C. difficile. Both are single-chain proteins with a similar multidomain architecture. Certain hypervirulent C. difficile strains also produce a third toxin, namely binary toxin CDT (C. difficile transferase). C. difficile toxins are the causative agents of C. difficile-associated diseases (CDADs), such as antibiotics-associated diarrhea and pseudomembranous colitis. For that reason, considerable efforts have been expended to unravel their molecular mode-of-action and the cellular mechanisms responsible for their uptake. Many of these studies have been conducted in European laboratories. Here, we provide an update on our previous review (Papatheodorou et al. Adv Exp Med Biol, 2018) on important advances in C. difficile toxins research.
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Affiliation(s)
- Panagiotis Papatheodorou
- Institute of Experimental and Clinical Pharmacology, Toxicology and Pharmacology of Natural Products, Ulm University Medical Center, Ulm, Germany.
| | - Nigel P Minton
- BBSRC/EPSRC Synthetic Biology Research Centre, University of Nottingham, Nottingham, UK
| | - Klaus Aktories
- Institute of Experimental and Clinical Pharmacology and Toxicology, University of Freiburg, Freiburg, Germany
| | - Holger Barth
- Institute of Experimental and Clinical Pharmacology, Toxicology and Pharmacology of Natural Products, Ulm University Medical Center, Ulm, Germany
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3
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Nagahama M, Takehara M, Seike S, Sakaguchi Y. Cellular Uptake and Cytotoxicity of Clostridium perfringens Iota-Toxin. Toxins (Basel) 2023; 15:695. [PMID: 38133199 PMCID: PMC10747272 DOI: 10.3390/toxins15120695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/08/2023] [Accepted: 12/09/2023] [Indexed: 12/23/2023] Open
Abstract
Clostridium perfringens iota-toxin is composed of two separate proteins: a binding protein (Ib) that recognizes a host cell receptor and promotes the cellular uptake of a catalytic protein and (Ia) possessing ADP-ribosyltransferase activity that induces actin cytoskeleton disorganization. Ib exhibits the overall structure of bacterial pore-forming toxins (PFTs). Lipolysis-stimulated lipoprotein receptor (LSR) is defined as a host cell receptor for Ib. The binding of Ib to LSR causes an oligomer formation of Ib in lipid rafts of plasma membranes, mediating the entry of Ia into the cytoplasm. Ia induces actin cytoskeleton disruption via the ADP-ribosylation of G-actin and causes cell rounding and death. The binding protein alone disrupts the cell membrane and induces cytotoxicity in sensitive cells. Host cells permeabilized by the pore formation of Ib are repaired by a Ca2+-dependent plasma repair pathway. This review shows that the cellular uptake of iota-toxin utilizes a pathway of plasma membrane repair and that Ib alone induces cytotoxicity.
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Affiliation(s)
- Masahiro Nagahama
- Department of Microbiology, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima 770-8514, Japan; (M.T.); (Y.S.)
| | - Masaya Takehara
- Department of Microbiology, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima 770-8514, Japan; (M.T.); (Y.S.)
| | - Soshi Seike
- Laboratory of Molecular Microbiological Science, Faculty of Pharmaceutical Sciences, Hiroshima International University, Kure, Hiroshima 737-0112, Japan;
| | - Yoshihiko Sakaguchi
- Department of Microbiology, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima 770-8514, Japan; (M.T.); (Y.S.)
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4
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Abstract
Biomolecular condensates are reversible compartments that form through a process called phase separation. Post-translational modifications like ADP-ribosylation can nucleate the formation of these condensates by accelerating the self-association of proteins. Poly(ADP-ribose) (PAR) chains are remarkably transient modifications with turnover rates on the order of minutes, yet they can be required for the formation of granules in response to oxidative stress, DNA damage, and other stimuli. Moreover, accumulation of PAR is linked with adverse phase transitions in neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. In this review, we provide a primer on how PAR is synthesized and regulated, the diverse structures and chemistries of ADP-ribosylation modifications, and protein-PAR interactions. We review substantial progress in recent efforts to determine the molecular mechanism of PAR-mediated phase separation, and we further delineate how inhibitors of PAR polymerases may be effective treatments for neurodegenerative pathologies. Finally, we highlight the need for rigorous biochemical interrogation of ADP-ribosylation in vivo and in vitro to clarify the exact pathway from PARylation to condensate formation.
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Affiliation(s)
- Kevin Rhine
- Program in Cell, Molecular, Developmental Biology, and Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Hana M Odeh
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - James Shorter
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - Sua Myong
- Program in Cell, Molecular, Developmental Biology, and Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Physics Frontier Center (Center for the Physics of Living Cells), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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5
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Dai F, Guo M, Shao Y, Li C. Novel secreted STPKLRR from Vibrio splendidus AJ01 promotes pathogen internalization via mediating tropomodulin phosphorylation dependent cytoskeleton rearrangement. PLoS Pathog 2023; 19:e1011419. [PMID: 37216400 DOI: 10.1371/journal.ppat.1011419] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/11/2023] [Indexed: 05/24/2023] Open
Abstract
We previously demonstrated that the flagellin of intracellular Vibrio splendidus AJ01 could be specifically identified by tropomodulin (Tmod) and further mediate p53-dependent coelomocyte apoptosis in the sea cucumber Apostichopus japonicus. In higher animals, Tmod serves as a regulator in stabilizing the actin cytoskeleton. However, the mechanism on how AJ01 breaks the AjTmod-stabilized cytoskeleton for internalization remains unclear. Here, we identified a novel AJ01 Type III secretion system (T3SS) effector of leucine-rich repeat-containing serine/threonine-protein kinase (STPKLRR) with five LRR domains and a serine/threonine kinase (STYKc) domain, which could specifically interact with tropomodulin domain of AjTmod. Furthermore, we found that STPKLRR directly phosphorylated AjTmod at serine 52 (S52) to reduce the binding stability between AjTmod and actin. After AjTmod dissociated from actin, the F-actin/G-actin ratio decreased to induce cytoskeletal rearrangement, which in turn promoted the internalization of AJ01. The STPKLRR knocked out strain could not phosphorylated AjTmod and displayed lower internalization capacity and pathogenic effect compared to AJ01. Overall, we demonstrated for the first time that the T3SS effector STPKLRR with kinase activity was a novel virulence factor in Vibrio and mediated self-internalization by targeting host AjTmod phosphorylation dependent cytoskeleton rearrangement, which provided a candidate target to control AJ01 infection in practice.
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Affiliation(s)
- Fa Dai
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, PR China
| | - Ming Guo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, PR China
| | - Yina Shao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, PR China
| | - Chenghua Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, PR China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China
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6
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Hou Y, Zeng H, Li Z, Feng N, Meng F, Xu Y, Li L, Shao F, Ding J. Structural mechanisms of calmodulin activation of Shigella effector OspC3 to ADP-riboxanate caspase-4/11 and block pyroptosis. Nat Struct Mol Biol 2023; 30:261-272. [PMID: 36624349 DOI: 10.1038/s41594-022-00888-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 11/03/2022] [Indexed: 01/11/2023]
Abstract
The caspase-4/11-GSDMD pyroptosis axis recognizes cytosolic lipopolysaccharide for antibacterial defenses. Shigella flexneri employs an OspC3 effector to block pyroptosis by catalyzing NAD+-dependent arginine ADP-riboxanation of caspase-4/11. Here, we identify Ca2+-free calmodulin (CaM) that binds and stimulates OspC3 ADP-riboxanase activity. Crystal structures of OspC3-CaM and OspC3-caspase-4 binary complexes reveal unique CaM binding to an OspC3 N-terminal domain featuring an ADP-ribosyltransferase-like fold and specific recognition of caspase-4 by an OspC3 ankryin repeat domain, respectively. CaM-OspC3-caspase-4 ternary complex structures show that NAD+ binding reorganizes the catalytic pocket, in which D231 and D177 activate the substrate arginine for initial ADP-ribosylation and ribosyl 2'-OH in the ADP-ribosylated arginine, respectively, for subsequent deamination. We also determine structures of unmodified and OspC3-ADP-riboxanated caspase-4. Mechanisms derived from this series of structures covering the entire process of OspC3 action are supported by biochemical analyses in vitro and functional validation in S. flexneri-infected mice.
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Affiliation(s)
- Yanjie Hou
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Huan Zeng
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- National Institute of Biological Sciences, Beijing, Beijing, China
| | - Zilin Li
- National Institute of Biological Sciences, Beijing, Beijing, China
- Research Unit of Pyroptosis and Immunity, Chinese Academy of Medical Sciences and National Institute of Biological Sciences, Beijing, China
| | - Na Feng
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Fanyi Meng
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yue Xu
- National Institute of Biological Sciences, Beijing, Beijing, China
- Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lin Li
- National Institute of Biological Sciences, Beijing, Beijing, China
| | - Feng Shao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- National Institute of Biological Sciences, Beijing, Beijing, China.
- Research Unit of Pyroptosis and Immunity, Chinese Academy of Medical Sciences and National Institute of Biological Sciences, Beijing, China.
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China.
| | - Jingjin Ding
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- National Institute of Biological Sciences, Beijing, Beijing, China.
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7
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Zhang K, Peng T, Tao X, Tian M, Li Y, Wang Z, Ma S, Hu S, Pan X, Xue J, Luo J, Wu Q, Fu Y, Li S. Structural insights into caspase ADPR deacylization catalyzed by a bacterial effector and host calmodulin. Mol Cell 2022; 82:4712-4726.e7. [PMID: 36423631 DOI: 10.1016/j.molcel.2022.10.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/29/2022] [Accepted: 10/27/2022] [Indexed: 11/24/2022]
Abstract
Programmed cell death and caspase proteins play a pivotal role in host innate immune response combating pathogen infections. Blocking cell death is employed by many bacterial pathogens as a universal virulence strategy. CopC family type III effectors, including CopC from an environmental pathogen Chromobacterium violaceum, utilize calmodulin (CaM) as a co-factor to inactivate caspases by arginine ADPR deacylization. However, the molecular basis of the catalytic and substrate/co-factor binding mechanism is unknown. Here, we determine successive cryo-EM structures of CaM-CopC-caspase-3 ternary complex in pre-reaction, transition, and post-reaction states, which elucidate a multistep enzymatic mechanism of CopC-catalyzed ADPR deacylization. Moreover, we capture a snapshot of the detachment of modified caspase-3 from CopC. These structural insights are validated by mutagenesis analyses of CopC-mediated ADPR deacylization in vitro and animal infection in vivo. Our study offers a structural framework for understanding the molecular basis of arginine ADPR deacylization catalyzed by the CopC family.
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Affiliation(s)
- Kuo Zhang
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China; Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Ting Peng
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518055, Guangdong, China
| | - Xinyuan Tao
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518055, Guangdong, China
| | - Miao Tian
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China; Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Yanxin Li
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518055, Guangdong, China
| | - Zhao Wang
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - Shuaifei Ma
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518055, Guangdong, China
| | - Shufan Hu
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518055, Guangdong, China
| | - Xing Pan
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Juan Xue
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Jiwei Luo
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Qiulan Wu
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - Yang Fu
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China.
| | - Shan Li
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
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8
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Belyy A, Lindemann F, Roderer D, Funk J, Bardiaux B, Protze J, Bieling P, Oschkinat H, Raunser S. Mechanism of threonine ADP-ribosylation of F-actin by a Tc toxin. Nat Commun 2022; 13:4202. [PMID: 35858890 PMCID: PMC9300711 DOI: 10.1038/s41467-022-31836-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/01/2022] [Indexed: 11/25/2022] Open
Abstract
Tc toxins deliver toxic enzymes into host cells by a unique injection mechanism. One of these enzymes is the actin ADP-ribosyltransferase TccC3, whose activity leads to the clustering of the cellular cytoskeleton and ultimately cell death. Here, we show in atomic detail how TccC3 modifies actin. We find that the ADP-ribosyltransferase does not bind to G-actin but interacts with two consecutive actin subunits of F-actin. The binding of TccC3 to F-actin occurs via an induced-fit mechanism that facilitates access of NAD+ to the nucleotide binding pocket. The following nucleophilic substitution reaction results in the transfer of ADP-ribose to threonine-148 of F-actin. We demonstrate that this site-specific modification of F-actin prevents its interaction with depolymerization factors, such as cofilin, which impairs actin network turnover and leads to steady actin polymerization. Our findings reveal in atomic detail a mechanism of action of a bacterial toxin through specific targeting and modification of F-actin. Entomopathogenic bacteria used for pest control secrete potent Tc toxins. Here, the authors combine biochemistry, solution and solid-state NMR spectroscopy and cryo-EM to show in atomic detail how the toxin disrupts the host cell cytoskeleton and kills the target cell.
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Affiliation(s)
- Alexander Belyy
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227, Dortmund, Germany
| | - Florian Lindemann
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Daniel Roderer
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227, Dortmund, Germany.,Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Johanna Funk
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227, Dortmund, Germany
| | - Benjamin Bardiaux
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Bioinformatics Unit, 25-28 Rue du Docteur Roux, F-75015, Paris, France
| | - Jonas Protze
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Peter Bieling
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227, Dortmund, Germany
| | - Hartmut Oschkinat
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125, Berlin, Germany.
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227, Dortmund, Germany.
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9
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Sakari M, Tran MT, Rossjohn J, Pulliainen AT, Beddoe T, Littler DR. Crystal structures of pertussis toxin with NAD+ and analogs provide structural insights into the mechanism of its cytosolic ADP-ribosylation activity. J Biol Chem 2022; 298:101892. [PMID: 35378130 PMCID: PMC9079181 DOI: 10.1016/j.jbc.2022.101892] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 11/19/2022] Open
Abstract
Bordetella pertussis is the causative agent of whooping cough, a highly contagious respiratory disease. Pertussis toxin (PT), a major virulence factor secreted by B. pertussis, is an AB5-type protein complex topologically related to cholera toxin. The PT protein complex is internalized by host cells and follows a retrograde trafficking route to the endoplasmic reticulum, where it subsequently dissociates. The released enzymatic S1 subunit is then translocated from the endoplasmic reticulum into the cytosol and subsequently ADP-ribosylates the inhibitory alpha-subunits (Gαi) of heterotrimeric G proteins, thus promoting dysregulation of G protein–coupled receptor signaling. However, the mechanistic details of the ADP-ribosylation activity of PT are not well understood. Here, we describe crystal structures of the S1 subunit in complex with nicotinamide adenine dinucleotide (NAD+), with NAD+ hydrolysis products ADP-ribose and nicotinamide, with NAD+ analog PJ34, and with a novel NAD+ analog formed upon S1 subunit crystallization with 3-amino benzamide and NAD+, which we name benzamide amino adenine dinucleotide. These crystal structures provide unprecedented insights into pre- and post-NAD+ hydrolysis steps of the ADP-ribosyltransferase activity of PT. We propose that these data may aid in rational drug design approaches and further development of PT-specific small-molecule inhibitors.
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Affiliation(s)
- Moona Sakari
- Institute of Biomedicine, Research Unit for Infection and Immunity, University of Turku, Turku, Finland
| | - Mai T Tran
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia; Institute of Infection and Immunity, School of Medicine, Cardiff University, Heath Park, Cardiff, Wales, United Kingdom
| | - Arto T Pulliainen
- Institute of Biomedicine, Research Unit for Infection and Immunity, University of Turku, Turku, Finland.
| | - Travis Beddoe
- Department of Animal, Plant and Soil Science and Centre for AgriBioscience, La Trobe University, Bundoora, Victoria, Australia.
| | - Dene R Littler
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
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10
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Peng T, Tao X, Xia Z, Hu S, Xue J, Zhu Q, Pan X, Zhang Q, Li S. Pathogen hijacks programmed cell death signaling by arginine ADPR-deacylization of caspases. Mol Cell 2022; 82:1806-1820.e8. [PMID: 35338844 DOI: 10.1016/j.molcel.2022.03.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/05/2022] [Accepted: 03/03/2022] [Indexed: 12/14/2022]
Abstract
Caspases are evolutionarily conserved cysteine proteases that are essential for regulating cell death and are involved in multiple development and disease processes, including immunity. Here, we show that the bacterial type III secretion system (T3SS) effector CopC (Chromobacterium outer protein C) from the environmental pathogen Chromobacterium violaceum attacks caspase-3/-7/-8/-9 by ADPR-deacylization to dysregulate programmed cell death, including apoptosis, necroptosis, and pyroptosis. This modification involves ADP-ribosylation- and deamination-mediated cyclization on Arg207 of caspase-3 by a mechanism that requires the eukaryote-specific protein calmodulin (CaM), leading to inhibition of caspase activity. The manipulation of cell death signaling by CopC is essential for the virulence of C. violaceum in a mouse infection model. CopC represents a family of enzymes existing in taxonomically diverse bacteria associated with a wide spectrum of eukaryotes ranging from humans to plants. The unique activity of CopC establishes a mechanism by which bacteria counteract host defenses through a previously unrecognized post-translational modification.
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Affiliation(s)
- Ting Peng
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xinyuan Tao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Zhujun Xia
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Shufan Hu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Juan Xue
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, China
| | - Qiuyu Zhu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xing Pan
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Qiang Zhang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Shan Li
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
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11
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Iyer S, Das C. The unity of opposites: Strategic interplay between bacterial effectors to regulate cellular homeostasis. J Biol Chem 2021; 297:101340. [PMID: 34695417 PMCID: PMC8605245 DOI: 10.1016/j.jbc.2021.101340] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 10/15/2021] [Accepted: 10/20/2021] [Indexed: 11/23/2022] Open
Abstract
Legionella pneumophila is a facultative intracellular pathogen that uses the Dot/Icm Type IV secretion system (T4SS) to translocate many effectors into its host and establish a safe, replicative lifestyle. The bacteria, once phagocytosed, reside in a vacuolar structure known as the Legionella-containing vacuole (LCV) within the host cells and rapidly subvert organelle trafficking events, block inflammatory responses, hijack the host ubiquitination system, and abolish apoptotic signaling. This arsenal of translocated effectors can manipulate the host factors in a multitude of different ways. These proteins also contribute to bacterial virulence by positively or negatively regulating the activity of one another. Such effector-effector interactions, direct and indirect, provide the delicate balance required to maintain cellular homeostasis while establishing itself within the host. This review summarizes the recent progress in our knowledge of the structure-function relationship and biochemical mechanisms of select effector pairs from Legionella that work in opposition to one another, while highlighting the diversity of biochemical means adopted by this intracellular pathogen to establish a replicative niche within host cells.
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Affiliation(s)
- Shalini Iyer
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA.
| | - Chittaranjan Das
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA.
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12
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Scafuri N, Soler MA, Spitaleri A, Rocchia W. Enhanced Molecular Dynamics Method to Efficiently Increase the Discrimination Capability of Computational Protein-Protein Docking. J Chem Theory Comput 2021; 17:7271-7280. [PMID: 34653335 PMCID: PMC8582249 DOI: 10.1021/acs.jctc.1c00789] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Protein–protein
docking typically consists of the generation
of putative binding conformations, which are subsequently ranked by
fast heuristic scoring functions. The simplicity of these functions
allows for computational efficiency but has severe repercussions on
their discrimination capabilities. In this work, we show the effectiveness
of suitable descriptors calculated along short scaled molecular dynamics
runs in recognizing the nearest-native bound conformation among a
set of putative structures generated by the HADDOCK tool for eight
protein–protein systems.
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Affiliation(s)
- Nicola Scafuri
- CONCEPT Lab, Istituto Italiano di Tecnologia (IIT), Via E. Melen, 83, I-16152 Genova, Italy
| | - Miguel A Soler
- CONCEPT Lab, Istituto Italiano di Tecnologia (IIT), Via E. Melen, 83, I-16152 Genova, Italy
| | - Andrea Spitaleri
- CONCEPT Lab, Istituto Italiano di Tecnologia (IIT), Via E. Melen, 83, I-16152 Genova, Italy
| | - Walter Rocchia
- CONCEPT Lab, Istituto Italiano di Tecnologia (IIT), Via E. Melen, 83, I-16152 Genova, Italy
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13
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Nagahama M, Kobayashi K, Takehara M. Cathepsin Release from Lysosomes Promotes Endocytosis of Clostridium perfringens Iota-Toxin. Toxins (Basel) 2021; 13:toxins13100721. [PMID: 34679014 PMCID: PMC8537257 DOI: 10.3390/toxins13100721] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/06/2021] [Accepted: 10/11/2021] [Indexed: 11/25/2022] Open
Abstract
Iota-toxin from Clostridium perfringens type E is a binary toxin composed of two independent proteins: actin-ADP-ribosylating enzyme component, iota-a (Ia), and binding component, iota-b (Ib). Ib binds to target cell receptors and mediates the internalization of Ia into the cytoplasm. Extracellular lysosomal enzyme acid sphingomyelinase (ASMase) was previously shown to facilitate the internalization of iota-toxin. In this study, we investigated how lysosomal cathepsin promotes the internalization of iota-toxin into target cells. Cysteine protease inhibitor E64 prevented the cytotoxicity caused by iota-toxin, but aspartate protease inhibitor pepstatin-A and serine protease inhibitor AEBSF did not. Knockdown of lysosomal cysteine protease cathepsins B and L decreased the toxin-induced cytotoxicity. E64 suppressed the Ib-induced ASMase activity in extracellular fluid, showing that the proteases play a role in ASMase activation. These results indicate that cathepsin B and L facilitate entry of iota-toxin via activation of ASMase.
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14
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Schuller M, Butler RE, Ariza A, Tromans-Coia C, Jankevicius G, Claridge TDW, Kendall SL, Goh S, Stewart GR, Ahel I. Molecular basis for DarT ADP-ribosylation of a DNA base. Nature 2021; 596:597-602. [PMID: 34408320 DOI: 10.1038/s41586-021-03825-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 07/15/2021] [Indexed: 02/07/2023]
Abstract
ADP-ribosyltransferases use NAD+ to catalyse substrate ADP-ribosylation1, and thereby regulate cellular pathways or contribute to toxin-mediated pathogenicity of bacteria2-4. Reversible ADP-ribosylation has traditionally been considered a protein-specific modification5, but recent in vitro studies have suggested nucleic acids as targets6-9. Here we present evidence that specific, reversible ADP-ribosylation of DNA on thymidine bases occurs in cellulo through the DarT-DarG toxin-antitoxin system, which is found in a variety of bacteria (including global pathogens such as Mycobacterium tuberculosis, enteropathogenic Escherichia coli and Pseudomonas aeruginosa)10. We report the structure of DarT, which identifies this protein as a diverged member of the PARP family. We provide a set of high-resolution structures of this enzyme in ligand-free and pre- and post-reaction states, which reveals a specialized mechanism of catalysis that includes a key active-site arginine that extends the canonical ADP-ribosyltransferase toolkit. Comparison with PARP-HPF1, a well-established DNA repair protein ADP-ribosylation complex, offers insights into how the DarT class of ADP-ribosyltransferases evolved into specific DNA-modifying enzymes. Together, our structural and mechanistic data provide details of this PARP family member and contribute to a fundamental understanding of the ADP-ribosylation of nucleic acids. We also show that thymine-linked ADP-ribose DNA adducts reversed by DarG antitoxin (functioning as a noncanonical DNA repair factor) are used not only for targeted DNA damage to induce toxicity, but also as a signalling strategy for cellular processes. Using M. tuberculosis as an exemplar, we show that DarT-DarG regulates growth by ADP-ribosylation of DNA at the origin of chromosome replication.
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Affiliation(s)
- Marion Schuller
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Rachel E Butler
- Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, UK
| | - Antonio Ariza
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | | | - Gytis Jankevicius
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Biozentrum, University of Basel, Basel, Switzerland
| | - Tim D W Claridge
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Sharon L Kendall
- Centre for Emerging, Endemic and Exotic Disease, Pathology and Population Sciences, The Royal Veterinary College, Hatfield, UK
| | - Shan Goh
- Centre for Emerging, Endemic and Exotic Disease, Pathology and Population Sciences, The Royal Veterinary College, Hatfield, UK
| | - Graham R Stewart
- Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, UK.
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
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15
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Mills A, Gago F. On the Need to Tell Apart Fraternal Twins eEF1A1 and eEF1A2, and Their Respective Outfits. Int J Mol Sci 2021; 22:6973. [PMID: 34203525 PMCID: PMC8268798 DOI: 10.3390/ijms22136973] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/25/2021] [Accepted: 06/25/2021] [Indexed: 01/03/2023] Open
Abstract
eEF1A1 and eEF1A2 are paralogous proteins whose presence in most normal eukaryotic cells is mutually exclusive and developmentally regulated. Often described in the scientific literature under the collective name eEF1A, which stands for eukaryotic elongation factor 1A, their best known activity (in a monomeric, GTP-bound conformation) is to bind aminoacyl-tRNAs and deliver them to the A-site of the 80S ribosome. However, both eEF1A1 and eEF1A2 are endowed with multitasking abilities (sometimes performed by homo- and heterodimers) and can be located in different subcellular compartments, from the plasma membrane to the nucleus. Given the high sequence identity of these two sister proteins and the large number of post-translational modifications they can undergo, we are often confronted with the dilemma of discerning which is the particular proteoform that is actually responsible for the ascribed biochemical or cellular effects. We argue in this review that acquiring this knowledge is essential to help clarify, in molecular and structural terms, the mechanistic involvement of these two ancestral and abundant G proteins in a variety of fundamental cellular processes other than translation elongation. Of particular importance for this special issue is the fact that several de novo heterozygous missense mutations in the human EEF1A2 gene are associated with a subset of rare but severe neurological syndromes and cardiomyopathies.
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Affiliation(s)
| | - Federico Gago
- Department of Biomedical Sciences & “Unidad Asociada IQM-CSIC”, School of Medicine and Health Sciences, University of Alcalá, E-28805 Alcalá de Henares, Spain;
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16
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Yamada T, Tsuge H. Preparation of Clostridium perfringens binary iota-toxin pore complex for structural analysis using cryo-EM. Methods Enzymol 2021; 649:125-148. [PMID: 33712185 DOI: 10.1016/bs.mie.2021.01.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Iota toxin, a type of A-B toxin produced by Clostridium perfringens, comprises an enzymatic component (Ia) and a membrane-binding component (Ib). The translocation of Ia to the target cell via the pore formed by Ib allows it to function as an ADP-ribosyltransferase that inhibits actin polymerization in the host cell. The structure of Ia-bound Ib-pore has been determined using cryo-electron microscopy (cryo-EM), thereby elucidating the mechanism of the initial Ia translocation; however, open questions regarding Ia translocation still exist. In this chapter, we describe a new method of preparing Ia-bound Ib-pore complex samples for structural analysis at high resolution using cryo-EM. This method is different from previously reported methods for other A-B toxins. Consequently, it produces Ib-pore with two different states with short and long membrane-spanning β-barrel stem. We expect that this method will be useful in functional and structural studies of iota toxin and other binary toxins.
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Affiliation(s)
- Tomohito Yamada
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan.
| | - Hideaki Tsuge
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan; Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan; Center for Molecular Research in Infectious Diseases, Kyoto Sangyo University, Kyoto, Japan.
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17
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Chaoprasid P, Lukat P, Mühlen S, Heidler T, Gazdag E, Dong S, Bi W, Rüter C, Kirchenwitz M, Steffen A, Jänsch L, Stradal TEB, Dersch P, Blankenfeldt W. Crystal structure of bacterial cytotoxic necrotizing factor CNF Y reveals molecular building blocks for intoxication. EMBO J 2021; 40:e105202. [PMID: 33410511 PMCID: PMC7883292 DOI: 10.15252/embj.2020105202] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 11/12/2020] [Accepted: 11/23/2020] [Indexed: 12/30/2022] Open
Abstract
Cytotoxic necrotizing factors (CNFs) are bacterial single-chain exotoxins that modulate cytokinetic/oncogenic and inflammatory processes through activation of host cell Rho GTPases. To achieve this, they are secreted, bind surface receptors to induce endocytosis and translocate a catalytic unit into the cytosol to intoxicate host cells. A three-dimensional structure that provides insight into the underlying mechanisms is still lacking. Here, we determined the crystal structure of full-length Yersinia pseudotuberculosis CNFY . CNFY consists of five domains (D1-D5), and by integrating structural and functional data, we demonstrate that D1-3 act as export and translocation module for the catalytic unit (D4-5) and for a fused β-lactamase reporter protein. We further found that D4, which possesses structural similarity to ADP-ribosyl transferases, but had no equivalent catalytic activity, changed its position to interact extensively with D5 in the crystal structure of the free D4-5 fragment. This liberates D5 from a semi-blocked conformation in full-length CNFY , leading to higher deamidation activity. Finally, we identify CNF translocation modules in several uncharacterized fusion proteins, which suggests their usability as a broad-specificity protein delivery tool.
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Affiliation(s)
- Paweena Chaoprasid
- Institute of InfectiologyCenter for Molecular Biology of Inflammation (ZMBE)University of MünsterMünsterGermany
- Molecular Infection BiologyHelmholtz Centre for Infection ResearchBraunschweigGermany
| | - Peer Lukat
- Structure and Function of ProteinsHelmholtz Centre for Infection ResearchBraunschweigGermany
| | - Sabrina Mühlen
- Institute of InfectiologyCenter for Molecular Biology of Inflammation (ZMBE)University of MünsterMünsterGermany
- Molecular Infection BiologyHelmholtz Centre for Infection ResearchBraunschweigGermany
- Deutsches Zentrum für InfektionsforschungBraunschweigGermany
| | - Thomas Heidler
- Molecular Structural BiologyHelmholtz Centre for Infection ResearchBraunschweigGermany
| | - Emerich‐Mihai Gazdag
- Structure and Function of ProteinsHelmholtz Centre for Infection ResearchBraunschweigGermany
| | - Shuangshuang Dong
- Structure and Function of ProteinsHelmholtz Centre for Infection ResearchBraunschweigGermany
| | - Wenjie Bi
- Cellular ProteomicsHelmholtz Centre for Infection ResearchBraunschweigGermany
| | - Christian Rüter
- Institute of InfectiologyCenter for Molecular Biology of Inflammation (ZMBE)University of MünsterMünsterGermany
| | - Marco Kirchenwitz
- Cell BiologyHelmholtz Centre for Infection ResearchBraunschweigGermany
| | - Anika Steffen
- Cell BiologyHelmholtz Centre for Infection ResearchBraunschweigGermany
| | - Lothar Jänsch
- Cellular ProteomicsHelmholtz Centre for Infection ResearchBraunschweigGermany
- Institute of ZoologyTechnische Universität BraunschweigBraunschweigGermany
| | - Theresia E B Stradal
- Cell BiologyHelmholtz Centre for Infection ResearchBraunschweigGermany
- Institute of ZoologyTechnische Universität BraunschweigBraunschweigGermany
| | - Petra Dersch
- Institute of InfectiologyCenter for Molecular Biology of Inflammation (ZMBE)University of MünsterMünsterGermany
- Molecular Infection BiologyHelmholtz Centre for Infection ResearchBraunschweigGermany
- Deutsches Zentrum für InfektionsforschungBraunschweigGermany
- Institute of MicrobiologyTechnische Universität BraunschweigBraunschweigGermany
| | - Wulf Blankenfeldt
- Structure and Function of ProteinsHelmholtz Centre for Infection ResearchBraunschweigGermany
- Institute for Biochemistry, Biotechnology and BioinformaticsTechnische Universität BraunschweigBraunschweigGermany
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18
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Smith H, Pinkerton N, Heisler DB, Kudryashova E, Hall AR, Karch KR, Norris A, Wysocki V, Sotomayor M, Reisler E, Vavylonis D, Kudryashov DS. Rounding Out the Understanding of ACD Toxicity with the Discovery of Cyclic Forms of Actin Oligomers. Int J Mol Sci 2021; 22:E718. [PMID: 33450834 PMCID: PMC7828245 DOI: 10.3390/ijms22020718] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/30/2020] [Accepted: 01/09/2021] [Indexed: 11/17/2022] Open
Abstract
Actin is an essential element of both innate and adaptive immune systems and can aid in motility and translocation of bacterial pathogens, making it an attractive target for bacterial toxins. Pathogenic Vibrio and Aeromonas genera deliver actin cross-linking domain (ACD) toxin into the cytoplasm of the host cell to poison actin regulation and promptly induce cell rounding. At early stages of toxicity, ACD covalently cross-links actin monomers into oligomers (AOs) that bind through multivalent interactions and potently inhibit several families of actin assembly proteins. At advanced toxicity stages, we found that the terminal protomers of linear AOs can get linked together by ACD to produce cyclic AOs. When tested against formins and Ena/VASP, linear and cyclic AOs exhibit similar inhibitory potential, which for the cyclic AOs is reduced in the presence of profilin. In coarse-grained molecular dynamics simulations, profilin and WH2-motif binding sites on actin subunits remain exposed in modeled AOs of both geometries. We speculate, therefore, that the reduced toxicity of cyclic AOs is due to their reduced configurational entropy. A characteristic feature of cyclic AOs is that, in contrast to the linear forms, they cannot be straightened to form filaments (e.g., through stabilization by cofilin), which makes them less susceptible to neutralization by the host cell.
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Affiliation(s)
- Harper Smith
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; (H.S.); (N.P.); (D.B.H.); (E.K.); (K.R.K.); (A.N.); (V.W.); (M.S.)
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
| | - Nick Pinkerton
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; (H.S.); (N.P.); (D.B.H.); (E.K.); (K.R.K.); (A.N.); (V.W.); (M.S.)
| | - David B. Heisler
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; (H.S.); (N.P.); (D.B.H.); (E.K.); (K.R.K.); (A.N.); (V.W.); (M.S.)
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Elena Kudryashova
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; (H.S.); (N.P.); (D.B.H.); (E.K.); (K.R.K.); (A.N.); (V.W.); (M.S.)
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Aaron R. Hall
- Department of Physics, Lehigh University, Bethlehem, PA 18015, USA; (A.R.H.); (D.V.)
| | - Kelly R. Karch
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; (H.S.); (N.P.); (D.B.H.); (E.K.); (K.R.K.); (A.N.); (V.W.); (M.S.)
| | - Andrew Norris
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; (H.S.); (N.P.); (D.B.H.); (E.K.); (K.R.K.); (A.N.); (V.W.); (M.S.)
| | - Vicki Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; (H.S.); (N.P.); (D.B.H.); (E.K.); (K.R.K.); (A.N.); (V.W.); (M.S.)
| | - Marcos Sotomayor
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; (H.S.); (N.P.); (D.B.H.); (E.K.); (K.R.K.); (A.N.); (V.W.); (M.S.)
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Emil Reisler
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA;
| | - Dimitrios Vavylonis
- Department of Physics, Lehigh University, Bethlehem, PA 18015, USA; (A.R.H.); (D.V.)
| | - Dmitri S. Kudryashov
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; (H.S.); (N.P.); (D.B.H.); (E.K.); (K.R.K.); (A.N.); (V.W.); (M.S.)
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
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19
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Yoshida T, Tsuge H. Common Mechanism for Target Specificity of Protein- and DNA-Targeting ADP-Ribosyltransferases. Toxins (Basel) 2021; 13:toxins13010040. [PMID: 33430384 PMCID: PMC7827354 DOI: 10.3390/toxins13010040] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 01/01/2021] [Accepted: 01/03/2021] [Indexed: 12/14/2022] Open
Abstract
Many bacterial pathogens utilize ADP-ribosyltransferases (ARTs) as virulence factors. The critical aspect of ARTs is their target specificity. Each individual ART modifies a specific residue of its substrates, which could be proteins, DNA, or antibiotics. However, the mechanism underlying this specificity is poorly understood. Here, we review the substrate recognition mechanism and target residue specificity based on the available complex structures of ARTs and their substrates. We show that there are common mechanisms of target residue specificity among protein- and DNA-targeting ARTs.
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Affiliation(s)
- Toru Yoshida
- Faculty of Science, Japan Women’s University, 2-8-1 Mejirodai, Bunkyo-ku, Tokyo 112-8681, Japan;
| | - Hideaki Tsuge
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto 603-8555, Japan
- Institute for Protein Dynamics, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto 603-8555, Japan
- Center for Molecular Research in Infectious Diseases, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto 603-8555, Japan
- Correspondence: ; Tel.: +81-75-705-3117
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20
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Tremblay O, Thow Z, Merrill AR. Several New Putative Bacterial ADP-Ribosyltransferase Toxins Are Revealed from In Silico Data Mining, Including the Novel Toxin Vorin, Encoded by the Fire Blight Pathogen Erwinia amylovora. Toxins (Basel) 2020; 12:E792. [PMID: 33322547 PMCID: PMC7764402 DOI: 10.3390/toxins12120792] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 11/28/2020] [Accepted: 12/10/2020] [Indexed: 12/31/2022] Open
Abstract
Mono-ADP-ribosyltransferase (mART) toxins are secreted by several pathogenic bacteria that disrupt vital host cell processes in deadly diseases like cholera and whooping cough. In the last two decades, the discovery of mART toxins has helped uncover the mechanisms of disease employed by pathogens impacting agriculture, aquaculture, and human health. Due to the current abundance of mARTs in bacterial genomes, and an unprecedented availability of genomic sequence data, mART toxins are amenable to discovery using an in silico strategy involving a series of sequence pattern filters and structural predictions. In this work, a bioinformatics approach was used to discover six bacterial mART sequences, one of which was a functional mART toxin encoded by the plant pathogen, Erwinia amylovora, called Vorin. Using a yeast growth-deficiency assay, we show that wild-type Vorin inhibited yeast cell growth, while catalytic variants reversed the growth-defective phenotype. Quantitative mass spectrometry analysis revealed that Vorin may cause eukaryotic host cell death by suppressing the initiation of autophagic processes. The genomic neighbourhood of Vorin indicated that it is a Type-VI-secreted effector, and co-expression experiments showed that Vorin is neutralized by binding of a cognate immunity protein, VorinI. We demonstrate that Vorin may also act as an antibacterial effector, since bacterial expression of Vorin was not achieved in the absence of VorinI. Vorin is the newest member of the mART family; further characterization of the Vorin/VorinI complex may help refine inhibitor design for mART toxins from other deadly pathogens.
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Affiliation(s)
| | | | - A. Rod Merrill
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada; (O.T.); (Z.T.)
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21
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Biomimetic α-selective ribosylation enables two-step modular synthesis of biologically important ADP-ribosylated peptides. Nat Commun 2020; 11:5600. [PMID: 33154359 PMCID: PMC7645758 DOI: 10.1038/s41467-020-19409-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 10/07/2020] [Indexed: 12/22/2022] Open
Abstract
The α-type ADP-ribosylated peptides represent a class of important molecular tools in the field of protein ADP-ribosylation, however, they are difficult to access because of their inherent complicated structures and the lack of effective synthetic tools. In this paper, we present a biomimetic α-selective ribosylation reaction to synthesize a key intermediate, α-ADP-ribosyl azide, directly from native β-nicotinamide adenine dinucleotide in a clean ionic liquid system. This reaction in tandem with click chemistry then offers a two-step modular synthesis of α-ADP-ribosylated peptides. These syntheses can be performed open air in eppendorf tubes, without the need for specialized instruments or training. Importantly, we demonstrate that the synthesized α-ADP-ribosylated peptides show high binding affinity and desirable stability for enriching protein partners, and reactivity in post-stage poly ADP-ribosylations. Owing to their simple chemistry and multidimensional bio-applications, the presented methods may provide a powerful platform to produce general molecular tools for the study of protein ADP-ribosylation. ADP-ribosylated peptides are important molecular tools, however, the lack of effective synthetic methods hinders the access to their complex structures. Here, the authors present a biomimetic α-selective ribosylation reaction coupled with click chemistry ultimately providing a two-step modular synthesis of α-ADP-ribosylated peptides.
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22
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Chutshela A, Masamba P, Oyinloye BE, Kappo AP. Molecular Context of ADP-ribosylation in Schistosomes for Drug Discovery and Vaccine Development. Curr Drug Discov Technol 2020; 18:473-484. [PMID: 32767945 DOI: 10.2174/1570163817666200806170654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 07/06/2020] [Accepted: 07/06/2020] [Indexed: 11/22/2022]
Abstract
Schistosome infection is regarded as one of the most important and neglected tropical diseases associated with poor sanitation. Like other living organisms, schistosomes employ multiple biological processes, of which some are regulated by a post-translational modification called Adenosine Diphosphate-ribosylation (ADP-ribosylation), catalyzed by ADP-ribosyltransferases. ADP-ribosylation is the addition of ADP-ribose moieties from Nicotinamide Adenine Dinucleotide (NAD+) to various targets, which include proteins and nucleotides. It is crucial in biological processes such as DNA repair, apoptosis, carbohydrate metabolism and catabolism. In the absence of a vaccine against schistosomiasis, this becomes a promising pathway in the identification of drug targets against various forms of this infection. The tegument of the worm is an encouraging immunogenic target for anti-schistosomal vaccine development. Vaccinology, molecular modeling and target-based drug discovery strategies have been used for years in drug discovery and for vaccine development. In this paper, we outline ADP-ribosylation and other different approaches to drug discovery and vaccine development against schistosomiasis.
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Affiliation(s)
- Amandla Chutshela
- Department of Biochemistry and Microbiology, University of Zululand, KwaDlangezwa 3886, South Africa
| | - Priscilla Masamba
- Molecular Biophysics and Structural Biology Group, Department of Biochemistry, University of Johannesburg, Kingsway Campus, Auckland Park 2006, South Africa
| | | | - Abidemi Paul Kappo
- Molecular Biophysics and Structural Biology Group, Department of Biochemistry, University of Johannesburg, Kingsway Campus, Auckland Park 2006, South Africa
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23
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Nilov DK, Pushkarev SV, Gushchina IV, Manasaryan GA, Kirsanov KI, Švedas VK. Modeling of the Enzyme-Substrate Complexes of Human Poly(ADP-Ribose) Polymerase 1. BIOCHEMISTRY (MOSCOW) 2020; 85:99-107. [PMID: 32079521 DOI: 10.1134/s0006297920010095] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Poly(ADP-ribose) polymerase 1 (PARP-1) is a key DNA repair enzyme and an important target in cancer treatment. Conventional methods of studying the reaction mechanism of PARP-1 have limitations because of the complex structure of PARP-1 substrates; however, the necessary data can be obtained by molecular modeling. In this work, a molecular dynamics model for the PARP-1 enzyme-substrate complex containing NAD+ molecule and the end of the poly(ADP-ribose) chain in the form of ADP molecule was obtained for the first time. Interactions with the active site residues have been characterized where Gly863, Lys903, Glu988 play a crucial role, and the SN1-like mechanism for the enzymatic ADP-ribosylation reaction has been proposed. Models of PARP-1 complexes with more sophisticated two-unit fragments of the growing polymer chain as well as competitive inhibitors 3-aminobenzamide and 7-methylguanine have been obtained by molecular docking.
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Affiliation(s)
- D K Nilov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - S V Pushkarev
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119991, Russia
| | - I V Gushchina
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119991, Russia
| | - G A Manasaryan
- Lomonosov Moscow State University, Faculty of Fundamental Medicine, Moscow, 119991, Russia
| | - K I Kirsanov
- Blokhin National Medical Research Center of Oncology, Institute of Carcinogenesis, Moscow, 115478, Russia
| | - V K Švedas
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia. .,Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119991, Russia
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24
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Rustandi RR, Hamm M. Development of an ADP-ribosylation assay for residual toxicity in C. difficile binary toxin CDTa using automated capillary western blot. J Pharm Biomed Anal 2020; 182:113125. [DOI: 10.1016/j.jpba.2020.113125] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/16/2020] [Accepted: 01/22/2020] [Indexed: 01/05/2023]
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25
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Yamada T, Yoshida T, Kawamoto A, Mitsuoka K, Iwasaki K, Tsuge H. Cryo-EM structures reveal translocational unfolding in the clostridial binary iota toxin complex. Nat Struct Mol Biol 2020; 27:288-296. [PMID: 32123390 DOI: 10.1038/s41594-020-0388-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 01/17/2020] [Indexed: 11/09/2022]
Abstract
The iota toxin produced by Clostridium perfringens type E is a binary toxin comprising two independent polypeptides: Ia, an ADP-ribosyltransferase, and Ib, which is involved in cell binding and translocation of Ia across the cell membrane. Here we report cryo-EM structures of the translocation channel Ib-pore and its complex with Ia. The high-resolution Ib-pore structure demonstrates a similar structural framework to that of the catalytic ϕ-clamp of the anthrax protective antigen pore. However, the Ia-bound Ib-pore structure shows a unique binding mode of Ia: one Ia binds to the Ib-pore, and the Ia amino-terminal domain forms multiple weak interactions with two additional Ib-pore constriction sites. Furthermore, Ib-binding induces tilting and partial unfolding of the Ia N-terminal α-helix, permitting its extension to the ϕ-clamp gate. This new mechanism of N-terminal unfolding is crucial for protein translocation.
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Affiliation(s)
- Tomohito Yamada
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, Japan
| | - Toru Yoshida
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, Japan.,Institute for Protein Dynamics, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, Japan
| | - Akihiro Kawamoto
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Kaoru Mitsuoka
- Research Center for Ultra-High Voltage Electron Microscopy, Osaka University, Ibaraki, Osaka, Japan
| | - Kenji Iwasaki
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan.,Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Japan
| | - Hideaki Tsuge
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, Japan. .,Institute for Protein Dynamics, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, Japan. .,Center for Molecular Research in Infectious Diseases, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, Japan.
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26
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Hoch NC, Polo LM. ADP-ribosylation: from molecular mechanisms to human disease. Genet Mol Biol 2019; 43:e20190075. [PMID: 31930280 PMCID: PMC7198025 DOI: 10.1590/1678-4685-gmb-2019-0075] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 07/04/2019] [Indexed: 12/23/2022] Open
Abstract
Post-translational modification of proteins by ADP-ribosylation, catalysed by
poly (ADP-ribose) polymerases (PARPs) using NAD+ as a substrate,
plays central roles in DNA damage signalling and repair, modulates a range of
cellular signalling cascades and initiates programmed cell death by parthanatos.
Here, we present mechanistic aspects of ADP-ribose modification, PARP activation
and the cellular functions of ADP-ribose signalling, and discuss how this
knowledge is uncovering therapeutic avenues for the treatment of increasingly
prevalent human diseases such as cancer, ischaemic damage and
neurodegeneration.
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Affiliation(s)
- Nicolas C Hoch
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Luis M Polo
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK.,Institute of Histology and Embryology of Mendoza - CONICET, Mendoza, Argentina
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27
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Towards the application of Tc toxins as a universal protein translocation system. Nat Commun 2019; 10:5263. [PMID: 31748551 PMCID: PMC6868009 DOI: 10.1038/s41467-019-13253-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 10/28/2019] [Indexed: 11/25/2022] Open
Abstract
Tc toxins are bacterial protein complexes that inject cytotoxic enzymes into target cells using a syringe-like mechanism. Tc toxins are composed of a membrane translocator and a cocoon that encapsulates a toxic enzyme. The toxic enzyme varies between Tc toxins from different species and is not conserved. Here, we investigate whether the toxic enzyme can be replaced by other small proteins of different origin and properties, namely Cdc42, herpes simplex virus ICP47, Arabidopsis thaliana iLOV, Escherichia coli DHFR, Ras-binding domain of CRAF kinase, and TEV protease. Using a combination of electron microscopy, X-ray crystallography and in vitro translocation assays, we demonstrate that it is possible to turn Tc toxins into customizable molecular syringes for delivering proteins of interest across membranes. We also infer the guidelines that protein cargos must obey in terms of size, charge, and fold in order to apply Tc toxins as a universal protein translocation system. Tc toxins are a major class of bacterial toxin translocation systems that inject toxic enzymes into target cells. Here the authors present functional and structural data showing that the toxic enzyme can be replaced by other small proteins and identify prerequisites required for successful translocation, which could facilitate the development of functional Tc-based protein injection devices.
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28
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Lassak J, Koller F, Krafczyk R, Volkwein W. Exceptionally versatile – arginine in bacterial post-translational protein modifications. Biol Chem 2019; 400:1397-1427. [DOI: 10.1515/hsz-2019-0182] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 06/01/2019] [Indexed: 12/24/2022]
Abstract
Abstract
Post-translational modifications (PTM) are the evolutionary solution to challenge and extend the boundaries of genetically predetermined proteomic diversity. As PTMs are highly dynamic, they also hold an enormous regulatory potential. It is therefore not surprising that out of the 20 proteinogenic amino acids, 15 can be post-translationally modified. Even the relatively inert guanidino group of arginine is subject to a multitude of mostly enzyme mediated chemical changes. The resulting alterations can have a major influence on protein function. In this review, we will discuss how bacteria control their cellular processes and develop pathogenicity based on post-translational protein-arginine modifications.
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Affiliation(s)
- Jürgen Lassak
- Center for Integrated Protein Science Munich (CiPSM), Department of Biology I, Microbiology , Ludwig-Maximilians-Universität München , Grosshaderner Strasse 2-4 , D-82152 Planegg , Germany
| | - Franziska Koller
- Center for Integrated Protein Science Munich (CiPSM), Department of Biology I, Microbiology , Ludwig-Maximilians-Universität München , Grosshaderner Strasse 2-4 , D-82152 Planegg , Germany
| | - Ralph Krafczyk
- Center for Integrated Protein Science Munich (CiPSM), Department of Biology I, Microbiology , Ludwig-Maximilians-Universität München , Grosshaderner Strasse 2-4 , D-82152 Planegg , Germany
| | - Wolfram Volkwein
- Center for Integrated Protein Science Munich (CiPSM), Department of Biology I, Microbiology , Ludwig-Maximilians-Universität München , Grosshaderner Strasse 2-4 , D-82152 Planegg , Germany
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29
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Stiles BG. Clostridial Binary Toxins: Basic Understandings that Include Cell Surface Binding and an Internal "Coup de Grâce". Curr Top Microbiol Immunol 2019; 406:135-162. [PMID: 27380267 DOI: 10.1007/82_2016_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Clostridium species can make a remarkable number of different protein toxins, causing many diverse diseases in humans and animals. The binary toxins of Clostridium botulinum, C. difficile, C. perfringens, and C. spiroforme are one group of enteric-acting toxins that attack the actin cytoskeleton of various cell types. These enterotoxins consist of A (enzymatic) and B (cell binding/membrane translocation) components that assemble on the targeted cell surface or in solution, forming a multimeric complex. Once translocated into the cytosol via endosomal trafficking and acidification, the A component dismantles the filamentous actin-based cytoskeleton via mono-ADP-ribosylation of globular actin. Knowledge of cell surface receptors and how these usurped, host-derived molecules facilitate intoxication can lead to novel ways of defending against these clostridial binary toxins. A molecular-based understanding of the various steps involved in toxin internalization can also unveil therapeutic intervention points that stop the intoxication process. Furthermore, using these bacterial proteins as medicinal shuttle systems into cells provides intriguing possibilities in the future. The pertinent past and state-of-the-art present, regarding clostridial binary toxins, will be evident in this chapter.
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Affiliation(s)
- Bradley G Stiles
- Biology Department, Wilson College, Chambersburg, PA, 17201, USA.
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30
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Abstract
ADP-ribosylation (ADPr) is an ancient reversible modification of cellular macromolecules controlling major biological processes as diverse as DNA damage repair, transcriptional regulation, intracellular transport, immune and stress responses, cell survival and proliferation. Furthermore, enzymatic reactions of ADPr are central in the pathogenesis of many human diseases, including infectious conditions. By providing a review of ADPr signalling in bacterial systems, we highlight the relevance of this chemical modification in the pathogenesis of human diseases depending on host-pathogen interactions. The post-antibiotic era has raised the need to find alternative approaches to antibiotic administration, as major pathogens becoming resistant to antibiotics. An in-depth understanding of ADPr reactions provides the rationale for designing novel antimicrobial strategies for treatment of infectious diseases. In addition, the understanding of mechanisms of ADPr by bacterial virulence factors offers important hints to improve our knowledge on cellular processes regulated by eukaryotic homologous enzymes, which are often involved in the pathogenesis of human diseases.
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31
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Insights into the biogenesis, function, and regulation of ADP-ribosylation. Nat Chem Biol 2019; 14:236-243. [PMID: 29443986 DOI: 10.1038/nchembio.2568] [Citation(s) in RCA: 183] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 12/28/2017] [Indexed: 12/26/2022]
Abstract
ADP-ribosylation-the transfer of ADP-ribose (ADPr) from NAD+ onto target molecules-is catalyzed by members of the ADP-ribosyltransferase (ART) superfamily of proteins, found in all kingdoms of life. Modification of amino acids in protein targets by ADPr regulates critical cellular pathways in eukaryotes and underlies the pathogenicity of certain bacteria. Several members of the ART superfamily are highly relevant for disease; these include the poly(ADP-ribose) polymerases (PARPs), recently shown to be important cancer targets, and the bacterial toxins diphtheria toxin and cholera toxin, long known to be responsible for the symptoms of diphtheria and cholera that result in morbidity. In this Review, we discuss the functions of amino acid ADPr modifications and the ART proteins that make them, the nature of the chemical linkage between ADPr and its targets and how this impacts function and stability, and the way that ARTs select specific amino acids in targets to modify.
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32
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ParST is a widespread toxin-antitoxin module that targets nucleotide metabolism. Proc Natl Acad Sci U S A 2018; 116:826-834. [PMID: 30598453 DOI: 10.1073/pnas.1814633116] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Toxin-antitoxin (TA) systems interfere with essential cellular processes and are implicated in bacterial lifestyle adaptations such as persistence and the biofilm formation. Here, we present structural, biochemical, and functional data on an uncharacterized TA system, the COG5654-COG5642 pair. Bioinformatic analysis showed that this TA pair is found in 2,942 of the 16,286 distinct bacterial species in the RefSeq database. We solved a structure of the toxin bound to a fragment of the antitoxin to 1.50 Å. This structure suggested that the toxin is a mono-ADP-ribosyltransferase (mART). The toxin specifically modifies phosphoribosyl pyrophosphate synthetase (Prs), an essential enzyme in nucleotide biosynthesis conserved in all organisms. We propose renaming the toxin ParT for Prs ADP-ribosylating toxin and ParS for the cognate antitoxin. ParT is a unique example of an intracellular protein mART in bacteria and is the smallest known mART. This work demonstrates that TA systems can induce bacteriostasis through interference with nucleotide biosynthesis.
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33
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Puvar K, Luo ZQ, Das C. Uncovering the Structural Basis of a New Twist in Protein Ubiquitination. Trends Biochem Sci 2018; 44:467-477. [PMID: 30583962 DOI: 10.1016/j.tibs.2018.11.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 11/06/2018] [Accepted: 11/20/2018] [Indexed: 12/20/2022]
Abstract
Members of the SidE effector family from Legionella pneumophila represent a new paradigm in the ubiquitin world. These enzymes catalyze ubiquitination of target proteins via a mechanism different from that of conventional E1-E2-E3 biochemistry and play important roles in L. pneumophila virulence. They combine mono-ADP-ribosylation and phosphodiesterase activities to attach ubiquitin onto substrates, in great contrast to the orthodox pathway. A series of recent structural and mechanistic studies have clarified the action of these enzymes. Herein, we summarize the key insights into the structure and function of these proteins, emphasizing their modular nature, and discuss the biochemical implications of these proteins as well as areas of further exploration.
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Affiliation(s)
- Kedar Puvar
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47906, USA
| | - Zhao-Qing Luo
- Purdue Institute of Immunology, Inflammation, and Infectious Diseases and the Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47906, USA.
| | - Chittaranjan Das
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47906, USA.
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34
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Nagahama M, Takehara M, Kobayashi K. Interaction of Clostridium perfringens Iota Toxin and Lipolysis-Stimulated Lipoprotein Receptor (LSR). Toxins (Basel) 2018; 10:toxins10100405. [PMID: 30297616 PMCID: PMC6215307 DOI: 10.3390/toxins10100405] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 09/29/2018] [Accepted: 10/04/2018] [Indexed: 01/05/2023] Open
Abstract
Iota toxin produced by Clostridium perfringens is a binary, actin ADP-ribosylating toxin that is organized into the enzymatically active component Ia and the binding component Ib. Lipolysis-stimulated lipoprotein receptor (LSR) has been identified as a cellular receptor of Ib. Here, we investigated the functional interaction between Ib and LSR, where siRNA for LSR blocked the toxin-mediated cytotoxicity and the binding of Ib. The addition of Ib to LSR-green fluorescence protein (GFP)-transfected cells at 4 °C resulted in colocalization with LSR and Ib on the cell surface. Upon transfer of the cells from 4 °C to 37 °C, LSR and Ib were internalized and observed in cytoplasmic vesicles. When the cells were incubated with Ib at 37 °C and fractionated using the Triton-insoluble membrane, Ib oligomer was localized in insoluble factions that fulfilled the criteria of lipid rafts, and LSR was clustered in lipid rafts. To examine the interaction between N-terminal extracellular region of LSR and Ib, we constructed a series of LSR N-terminal deletions. Ten amino acids residues can be deleted from this end without any reduction of Ib binding. However, deletion of 15 N-terminal residues drastically reduces its ability to bind Ib. These results demonstrate that Ib binds to the LSR N-terminal 10 to 15 residues and endocytoses into trafficking endosomes together with LSR.
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Affiliation(s)
- Masahiro Nagahama
- Department of Microbiology, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima 770-8514, Japan.
| | - Masaya Takehara
- Department of Microbiology, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima 770-8514, Japan.
| | - Keiko Kobayashi
- Department of Microbiology, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima 770-8514, Japan.
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35
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Yoshida T, Tsuge H. Substrate N 2 atom recognition mechanism in pierisin family DNA-targeting, guanine-specific ADP-ribosyltransferase ScARP. J Biol Chem 2018; 293:13768-13774. [PMID: 30072382 DOI: 10.1074/jbc.ac118.004412] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 07/26/2018] [Indexed: 11/06/2022] Open
Abstract
ScARP from the bacterium Streptomyces coelicolor belongs to the pierisin family of DNA-targeting ADP-ribosyltransferases (ARTs). These enzymes ADP-ribosylate the N2 amino groups of guanine residues in DNA to yield N2-(ADP-ribos-1-yl)-2'-deoxyguanosine. Although the structures of pierisin-1 and Scabin were revealed recently, the substrate recognition mechanisms remain poorly understood because of the lack of a substrate-binding structure. Here, we report the apo structure of ScARP and of ScARP bound to NADH and its GDP substrate at 1.50 and 1.57 Å resolutions, respectively. The bound structure revealed that the guanine of GDP is trapped between N-ribose of NADH and Trp-159. Interestingly, N2 and N3 of guanine formed hydrogen bonds with the OE1 and NE2 atoms of Gln-162, respectively. We directly observed that the ADP-ribosylating toxin turn-turn (ARTT)-loop, including Trp-159 and Gln-162, plays a key role in the specificity of DNA-targeting, guanine-specific ARTs as well as protein-targeting ARTs such as the C3 exoenzyme. We propose that the ARTT-loop recognition is a common substrate-recognition mechanism in the pierisin family. Furthermore, this complex structure sheds light on similarities and differences among two subclasses that are distinguished by conserved structural motifs: H-Y-E in the ARTD subfamily and R-S-E in the ARTC subfamily. The spatial arrangements of the electrophile and nucleophile were the same, providing the first evidence for a common reaction mechanism in these ARTs. ARTC (including ScARP) uses the ARTT-loop for substrate recognition, whereas ARTD (represented by Arr) uses the C-terminal helix instead of the ARTT-loop. These observations could help inform efforts to improve ART inhibitors.
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Affiliation(s)
- Toru Yoshida
- From the Department of Bioresource and Environmental Sciences, Faculty of Life Sciences.,Institute for Protein Dynamics, and
| | - Hideaki Tsuge
- From the Department of Bioresource and Environmental Sciences, Faculty of Life Sciences, .,Institute for Protein Dynamics, and.,Center for Molecular Research in Infectious Diseases, Kyoto Sangyo University, Kyoto 603-8555, Japan
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36
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Kim L, Kwon DH, Kim BH, Kim J, Park MR, Park ZY, Song HK. Structural and Biochemical Study of the Mono-ADP-Ribosyltransferase Domain of SdeA, a Ubiquitylating/Deubiquitylating Enzyme from Legionella pneumophila. J Mol Biol 2018; 430:2843-2856. [PMID: 29870726 DOI: 10.1016/j.jmb.2018.05.043] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 05/24/2018] [Accepted: 05/27/2018] [Indexed: 11/18/2022]
Abstract
Conventional ubiquitylation occurs through an ATP-dependent three-enzyme cascade (E1, E2, and E3) that mediates the covalent conjugation of the C-terminus of ubiquitin to a lysine on the substrate. SdeA, which belongs to the SidE effector family of Legionella pneumophila, can transfer ubiquitin to endoplasmic reticulum-associated Rab-family GTPases in a manner independent of E1 and E2 enzymes. The novel ubiquitin-modifying enzyme SdeA utilizes NAD+ as a cofactor to attach ubiquitin to a serine residue of the substrate. Here, to elucidate the coupled enzymatic reaction of NAD+ hydrolysis and ADP-ribosylation of ubiquitin in SdeA, we characterized the mono-ADP-ribosyltransferase domain of SdeA and show that it consists of two sub-domains termed mART-N and mART-C. The crystal structure of the mART-C domain of SdeA was also determined in free form and in complex with NAD+ at high resolution. Furthermore, the spatial orientations of the N-terminal deubiquitylase, phosphodiesterase, mono-ADP-ribosyltransferase, and C-terminal coiled-coil domains within the 180-kDa full-length SdeA were determined. These results provide insight into the unusual ubiquitylation mechanism of SdeA and expand our knowledge on the structure-function of mono-ADP-ribosyltransferases.
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Affiliation(s)
- Leehyeon Kim
- Department of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea
| | - Do Hoon Kwon
- Department of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea
| | - Bong Heon Kim
- Department of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea
| | - Jiyeon Kim
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Mi Rae Park
- Department of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea
| | - Zee-Yong Park
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Hyun Kyu Song
- Department of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea.
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Mechanism of phosphoribosyl-ubiquitination mediated by a single Legionella effector. Nature 2018; 557:729-733. [PMID: 29795346 PMCID: PMC5980775 DOI: 10.1038/s41586-018-0147-6] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 04/18/2018] [Indexed: 11/08/2022]
Abstract
Ubiquitination is a post-translational modification that regulates many cellular processes in eukaryotes1-4. The conventional ubiquitination cascade culminates in a covalent linkage between the C terminus of ubiquitin (Ub) and a target protein, usually on a lysine side chain1,5. Recent studies of the Legionella pneumophila SidE family of effector proteins revealed a ubiquitination method in which a phosphoribosyl ubiquitin (PR-Ub) is conjugated to a serine residue on substrates via a phosphodiester bond6-8. Here we present the crystal structure of a fragment of the SidE family member SdeA that retains ubiquitination activity, and determine the mechanism of this unique post-translational modification. The structure reveals that the catalytic module contains two distinct functional units: a phosphodiesterase domain and a mono-ADP-ribosyltransferase domain. Biochemical analysis shows that the mono-ADP-ribosyltransferase domain-mediated conversion of Ub to ADP-ribosylated Ub (ADPR-Ub) and the phosphodiesterase domain-mediated ligation of PR-Ub to substrates are two independent activities of SdeA. Furthermore, we present two crystal structures of a homologous phosphodiesterase domain from the SidE family member SdeD 9 in complexes with Ub and ADPR-Ub. The structures suggest a mechanism for how SdeA processes ADPR-Ub to PR-Ub and AMP, and conjugates PR-Ub to a serine residue in substrates. Our study establishes the molecular mechanism of phosphoribosyl-linked ubiquitination and will enable future studies of this unusual type of ubiquitination in eukaryotes.
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Structural basis of ubiquitin modification by the Legionella effector SdeA. Nature 2018; 557:674-678. [PMID: 29795342 DOI: 10.1038/s41586-018-0146-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Accepted: 03/28/2018] [Indexed: 01/17/2023]
Abstract
Protein ubiquitination is a multifaceted post-translational modification that controls almost every process in eukaryotic cells. Recently, the Legionella effector SdeA was reported to mediate a unique phosphoribosyl-linked ubiquitination through successive modifications of the Arg42 of ubiquitin (Ub) by its mono-ADP-ribosyltransferase (mART) and phosphodiesterase (PDE) domains. However, the mechanisms of SdeA-mediated Ub modification and phosphoribosyl-linked ubiquitination remain unknown. Here we report the structures of SdeA in its ligand-free, Ub-bound and Ub-NADH-bound states. The structures reveal that the mART and PDE domains of SdeA form a catalytic domain over its C-terminal region. Upon Ub binding, the canonical ADP-ribosyltransferase toxin turn-turn (ARTT) and phosphate-nicotinamide (PN) loops in the mART domain of SdeA undergo marked conformational changes. The Ub Arg72 might act as a 'probe' that interacts with the mART domain first, and then movements may occur in the side chains of Arg72 and Arg42 during the ADP-ribosylation of Ub. Our study reveals the mechanism of SdeA-mediated Ub modification and provides a framework for further investigations into the phosphoribosyl-linked ubiquitination process.
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Nagahama M, Takehara M, Miyamoto K, Ishidoh K, Kobayashi K. Acid Sphingomyelinase Promotes Cellular Internalization of Clostridium perfringens Iota-Toxin. Toxins (Basel) 2018; 10:toxins10050209. [PMID: 29783772 PMCID: PMC5983265 DOI: 10.3390/toxins10050209] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 05/14/2018] [Accepted: 05/18/2018] [Indexed: 11/16/2022] Open
Abstract
Clostridium perfringens iota-toxin is a binary actin-ADP-ribosylating toxin composed of the enzymatic component Ia and receptor binding component Ib. Ib binds to a cell surface receptor, forms Ib oligomer in lipid rafts, and associates with Ia. The Ia-Ib complex then internalizes by endocytosis. Here, we showed that acid sphingomyelinase (ASMase) facilitates the cellular uptake of iota-toxin. Inhibitions of ASMase and lysosomal exocytosis by respective blockers depressed cell rounding induced by iota-toxin. The cytotoxicity of the toxin increased in the presence of Ca2+ in extracellular fluids. Ib entered target cells in the presence but not the absence of Ca2+. Ib induced the extracellular release of ASMase in the presence of Ca2+. ASMase siRNA prevented the cell rounding induced by iota-toxin. Furthermore, treatment of the cells with Ib resulted in the production of ceramide in cytoplasmic vesicles. These observations showed that ASMase promotes the internalization of iota-toxin into target cells.
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Affiliation(s)
- Masahiro Nagahama
- Department of Microbiology, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima 770-8514, Japan.
| | - Masaya Takehara
- Department of Microbiology, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima 770-8514, Japan.
| | - Kazuaki Miyamoto
- Department of Microbiology, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima 770-8514, Japan.
| | - Kazumi Ishidoh
- Division of Molecular Biology, Institute for Health Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima 770-8514, Japan.
| | - Keiko Kobayashi
- Department of Microbiology, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima 770-8514, Japan.
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Cellular Uptake and Mode-of-Action of Clostridium difficile Toxins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1050:77-96. [DOI: 10.1007/978-3-319-72799-8_6] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Small-Molecule Inhibitors of PARPs: From Tools for Investigating ADP-Ribosylation to Therapeutics. Curr Top Microbiol Immunol 2018; 420:211-231. [PMID: 30242511 DOI: 10.1007/82_2018_137] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Over the last 60 years, poly-ADP-ribose polymerases (PARPs, 17 family members in humans) have emerged as important regulators of physiology and disease. Small-molecule inhibitors have been essential tools for unraveling PARP function, and recently the first PARP inhibitors have been approved for the treatment of various human cancers. However, inhibitors have only been developed for a few PARPs and in vitro profiling has revealed that many of these exhibit polypharmacology across the PARP family. In this review, we discuss the history, development, and current state of the field, highlighting the limitations and opportunities for PARP inhibitor development.
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Lüscher B, Bütepage M, Eckei L, Krieg S, Verheugd P, Shilton BH. ADP-Ribosylation, a Multifaceted Posttranslational Modification Involved in the Control of Cell Physiology in Health and Disease. Chem Rev 2017; 118:1092-1136. [PMID: 29172462 DOI: 10.1021/acs.chemrev.7b00122] [Citation(s) in RCA: 169] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Posttranslational modifications (PTMs) regulate protein functions and interactions. ADP-ribosylation is a PTM, in which ADP-ribosyltransferases use nicotinamide adenine dinucleotide (NAD+) to modify target proteins with ADP-ribose. This modification can occur as mono- or poly-ADP-ribosylation. The latter involves the synthesis of long ADP-ribose chains that have specific properties due to the nature of the polymer. ADP-Ribosylation is reversed by hydrolases that cleave the glycosidic bonds either between ADP-ribose units or between the protein proximal ADP-ribose and a given amino acid side chain. Here we discuss the properties of the different enzymes associated with ADP-ribosylation and the consequences of this PTM on substrates. Furthermore, the different domains that interpret either mono- or poly-ADP-ribosylation and the implications for cellular processes are described.
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Affiliation(s)
- Bernhard Lüscher
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University , 52057 Aachen, Germany
| | - Mareike Bütepage
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University , 52057 Aachen, Germany
| | - Laura Eckei
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University , 52057 Aachen, Germany
| | - Sarah Krieg
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University , 52057 Aachen, Germany
| | - Patricia Verheugd
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University , 52057 Aachen, Germany
| | - Brian H Shilton
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University , 52057 Aachen, Germany.,Department of Biochemistry, Schulich School of Medicine & Dentistry, The University of Western Ontario , Medical Sciences Building Room 332, London, Ontario Canada N6A 5C1
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An Enterotoxin-Like Binary Protein from Pseudomonas protegens with Potent Nematicidal Activity. Appl Environ Microbiol 2017; 83:AEM.00942-17. [PMID: 28733289 PMCID: PMC5601331 DOI: 10.1128/aem.00942-17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 07/05/2017] [Indexed: 11/20/2022] Open
Abstract
Soil microbes are a major food source for free-living soil nematodes. It is known that certain soil bacteria have evolved systems to combat predation. We identified the nematode-antagonistic Pseudomonas protegens strain 15G2 from screening of microbes. Through protein purification we identified a binary protein, designated Pp-ANP, which is responsible for the nematicidal activity. This binary protein inhibits Caenorhabditis elegans growth and development by arresting larvae at the L1 stage and killing older-staged worms. The two subunits, Pp-ANP1a and Pp-ANP2a, are active when reconstituted from separate expression in Escherichia coli. The binary toxin also shows strong nematicidal activity against three other free-living nematodes (Pristionchus pacificus, Panagrellus redivivus, and Acrobeloides sp.), but we did not find any activity against insects and fungi under test conditions, indicating specificity for nematodes. Pp-ANP1a has no significant identity to any known proteins, while Pp-ANP2a shows ∼30% identity to E. coli heat-labile enterotoxin (LT) subunit A and cholera toxin (CT) subunit A. Protein modeling indicates that Pp-ANP2a is structurally similar to CT/LT and likely acts as an ADP-ribosyltransferase. Despite the similarity, Pp-ANP shows several characteristics distinct from CT/LT toxins. Our results indicate that Pp-ANP is a new enterotoxin-like binary toxin with potent and specific activity to nematodes. The potency and specificity of Pp-ANP suggest applications in controlling parasitic nematodes and open an avenue for further research on its mechanism of action and role in bacterium-nematode interaction. IMPORTANCE This study reports the discovery of a new enterotoxin-like binary protein, Pp-ANP, from a Pseudomonas protegens strain. Pp-ANP shows strong nematicidal activity against Caenorhabditis elegans larvae and older-staged worms. It also shows strong activity on other free-living nematodes (Pristionchus pacificus, Panagrellus redivivus, and Acrobeloides sp.). The two subunits, Pp-ANP1a and Pp-ANP2a, can be expressed separately and reconstituted to form the active complex. Pp-ANP shows some distinct characteristics compared with other toxins, including Escherichia coli enterotoxin and cholera toxin. The present study indicates that Pp-ANP is a novel binary toxin and that it has potential applications in controlling parasitic nematodes and in studying toxin-host interaction.
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Takehara M, Takagishi T, Seike S, Oda M, Sakaguchi Y, Hisatsune J, Ochi S, Kobayashi K, Nagahama M. Cellular Entry of Clostridium perfringens Iota-Toxin and Clostridium botulinum C2 Toxin. Toxins (Basel) 2017; 9:toxins9080247. [PMID: 28800062 PMCID: PMC5577581 DOI: 10.3390/toxins9080247] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 07/31/2017] [Accepted: 08/09/2017] [Indexed: 12/05/2022] Open
Abstract
Clostridium perfringens iota-toxin and Clostridium botulinum C2 toxin are composed of two non-linked proteins, one being the enzymatic component and the other being the binding/translocation component. These latter components recognize specific receptors and oligomerize in plasma membrane lipid-rafts, mediating the uptake of the enzymatic component into the cytosol. Enzymatic components induce actin cytoskeleton disorganization through the ADP-ribosylation of actin and are responsible for cell rounding and death. This review focuses upon the recent advances in cellular internalization of clostridial binary toxins.
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Affiliation(s)
- Masaya Takehara
- Department of Microbiology, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima 770-8514, Japan.
| | - Teruhisa Takagishi
- Department of Microbiology, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima 770-8514, Japan.
| | - Soshi Seike
- Laboratory of Molecular Microbiological Science, Faculty of Pharmaceutical Sciences, Hiroshima International University, Kure, Hiroshima 737-0112, Japan.
| | - Masataka Oda
- Department of Microbiology and Infection Control Science, Kyoto Pharmaceutical University, Yamashina, Kyoto 607-8414, Japan.
| | - Yoshihiko Sakaguchi
- Department of Microbiology, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0374, Japan.
| | - Junzo Hisatsune
- Department of Bacteriology, Graduate school of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8551, Japan.
| | - Sadayuki Ochi
- Faculty of Pharmacy, Yokohama University of Pharmacy, 601 Matano-cho, Totsuka-ku, Yokohama-shi, Kanagawa 245-0066, Japan.
| | - Keiko Kobayashi
- Department of Microbiology, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima 770-8514, Japan.
| | - Masahiro Nagahama
- Department of Microbiology, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima 770-8514, Japan.
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Littler DR, Ang SY, Moriel DG, Kocan M, Kleifeld O, Johnson MD, Tran MT, Paton AW, Paton JC, Summers RJ, Schembri MA, Rossjohn J, Beddoe T. Structure-function analyses of a pertussis-like toxin from pathogenic Escherichia coli reveal a distinct mechanism of inhibition of trimeric G-proteins. J Biol Chem 2017; 292:15143-15158. [PMID: 28663369 DOI: 10.1074/jbc.m117.796094] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 06/14/2017] [Indexed: 11/06/2022] Open
Abstract
Pertussis-like toxins are secreted by several bacterial pathogens during infection. They belong to the AB5 virulence factors, which bind to glycans on host cell membranes for internalization. Host cell recognition and internalization are mediated by toxin B subunits sharing a unique pentameric ring-like assembly. Although the role of pertussis toxin in whooping cough is well-established, pertussis-like toxins produced by other bacteria are less studied, and their mechanisms of action are unclear. Here, we report that some extra-intestinal Escherichia coli pathogens (i.e. those that reside in the gut but can spread to other bodily locations) encode a pertussis-like toxin that inhibits mammalian cell growth in vitro We found that this protein, EcPlt, is related to toxins produced by both nontyphoidal and typhoidal Salmonella serovars. Pertussis-like toxins are secreted as disulfide-bonded heterohexamers in which the catalytic ADP-ribosyltransferase subunit is activated when exposed to the reducing environment in mammalian cells. We found here that the reduced EcPlt exhibits large structural rearrangements associated with its activation. We noted that inhibitory residues tethered within the NAD+-binding site by an intramolecular disulfide in the oxidized state dissociate upon the reduction and enable loop restructuring to form the nucleotide-binding site. Surprisingly, although pertussis toxin targets a cysteine residue within the α subunit of inhibitory trimeric G-proteins, we observed that activated EcPlt toxin modifies a proximal lysine/asparagine residue instead. In conclusion, our results reveal the molecular mechanism underpinning activation of pertussis-like toxins, and we also identified differences in host target specificity.
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Affiliation(s)
- Dene R Littler
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Sheng Y Ang
- the Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Danilo G Moriel
- the School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Martina Kocan
- the Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Oded Kleifeld
- the Faculty of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Matthew D Johnson
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Mai T Tran
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Adrienne W Paton
- the Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia
| | - James C Paton
- the Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia
| | - Roger J Summers
- the Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Mark A Schembri
- the School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jamie Rossjohn
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia, .,the Institute of Infection and Immunity, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, Wales, United Kingdom.,the ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia, and
| | - Travis Beddoe
- the Department of Animal, Plant and Soil Science and Centre for AgriBioscience, La Trobe University, Bundoora, Victoria 3086, Australia
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Comparative Studies of Actin- and Rho-Specific ADP-Ribosylating Toxins: Insight from Structural Biology. Curr Top Microbiol Immunol 2017; 399:69-86. [PMID: 27540723 DOI: 10.1007/82_2016_23] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Mono-ADP-ribosylation is a major post-translational modification performed by bacterial toxins, which transfer an ADP-ribose moiety to a substrate acceptor residue. Actin- and Rho-specific ADP-ribosylating toxins (ARTs) are typical ARTs known to have very similar tertiary structures but totally different targets. Actin-specific ARTs are the A components of binary toxins, ADP-ribosylate actin at Arg177, leading to the depolymerization of the actin cytoskeleton. On the other hand, C3-like exoenzymes are Rho-specific ARTs, ADP-ribosylate Rho GTPases at Asn41, exerting an indirect effect on the actin cytoskeleton. This review focuses on the differences and similarities of actin- and Rho-specific ARTs, especially with respect to their substrate recognition and cell entry mechanisms, based on structural studies.
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Crystal structure and structure-based mutagenesis of actin-specific ADP-ribosylating toxin CPILE-a as novel enterotoxin. PLoS One 2017; 12:e0171278. [PMID: 28199340 PMCID: PMC5310789 DOI: 10.1371/journal.pone.0171278] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 01/17/2017] [Indexed: 01/07/2023] Open
Abstract
Unusual outbreaks of food poisoning in Japan were reported in which Clostridium perfringens was strongly suspected to be the cause based on epidemiological information and fingerprinting of isolates. The isolated strains lack the typical C. perfringens enterotoxin (CPE) but secrete a new enterotoxin consisting of two components: C. perfringens iota-like enterotoxin-a (CPILE-a), which acts as an enzymatic ADP-ribosyltransferase, and CPILE-b, a membrane binding component. Here we present the crystal structures of apo-CPILE-a, NAD+-CPILE-a and NADH-CPILE-a. Though CPILE-a structure has high similarity with known iota toxin-a (Ia) with NAD+, it possesses two extra-long protruding loops from G262-S269 and E402-K408 that are distinct from Ia. Based on the Ia-actin complex structure, we focused on actin-binding interface regions (I-V) including two protruding loops (PT) and examined how mutations in these regions affect the ADP-ribosylation activity of CPILE-a. Though some site-directed mutagenesis studies have already been conducted on the actin binding site of Ia, in the present study, mutagenesis studies were conducted against both α- and β/γ-actin in CPILE-a and Ia. Interestingly, CPILE-a ADP-ribosylates both α- and β/γ-actin, but its sensitivity towards β/γ-actin is 36% compared with α-actin. Our results contrast to that only C2-I ADP-ribosylates β/γ-actin. We also showed that PT-I and two convex-concave interactions in CPILE-a are important for actin binding. The current study is the first detailed analysis of site-directed mutagenesis in the actin binding region of Ia and CPILE-a against both α- and β/γ-actin.
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Crystal structure of the ADP-ribosylating component of BEC, the binary enterotoxin of Clostridium perfringens. Biochem Biophys Res Commun 2016; 480:261-267. [PMID: 27751850 DOI: 10.1016/j.bbrc.2016.10.042] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 10/14/2016] [Indexed: 11/20/2022]
Abstract
Binary enterotoxin of Clostridium perfringens (BEC), consisting of the components BECa and BECb, was recently identified as a novel enterotoxin produced by C. perfringens that causes acute gastroenteritis in humans. Although the detailed mechanism of cell intoxication by BEC remains to be defined, BECa shows both NAD+-glycohydrolase and actin ADP-ribosyltransferase activities in the presence of NAD+. In this study, we determined the first crystal structure of BECa in its apo-state and in complex with NADH. The structure of BECa shows striking resemblance with other binary actin ADP-ribosylating toxins (ADPRTs), especially in terms of its overall protein fold and mechanisms of substrate recognition. We present a detailed picture of interactions between BECa and NADH, including bound water molecules located near the C1'-N glycosidic bond of NADH and the catalytically important ADP-ribosylating turn-turn (ARTT) loop. We observed that the conformational rearrangement of the ARTT loop, possibly triggered by a conformational change involving a conserved tyrosine residue coupled with substrate binding, plays a crucial role in catalysis by properly positioning a catalytic glutamate residue in the E-X-E motif of the ARTT loop in contact with the nucleophile. Our results for BECa provide insight into the common catalytic mechanism of the family of binary actin ADPRTs.
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49
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Lyons B, Ravulapalli R, Lanoue J, Lugo MR, Dutta D, Carlin S, Merrill AR. Scabin, a Novel DNA-acting ADP-ribosyltransferase from Streptomyces scabies. J Biol Chem 2016; 291:11198-215. [PMID: 27002155 PMCID: PMC4900268 DOI: 10.1074/jbc.m115.707653] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 03/12/2016] [Indexed: 11/06/2022] Open
Abstract
A bioinformatics strategy was used to identify Scabin, a novel DNA-targeting enzyme from the plant pathogen 87.22 strain of Streptomyces scabies Scabin shares nearly 40% sequence identity with the Pierisin family of mono-ADP-ribosyltransferase toxins. Scabin was purified to homogeneity as a 22-kDa single-domain enzyme and was shown to possess high NAD(+)-glycohydrolase (Km (NAD) = 68 ± 3 μm; kcat = 94 ± 2 min(-1)) activity with an RSQXE motif; it was also shown to target deoxyguanosine and showed sigmoidal enzyme kinetics (K0.5(deoxyguanosine) = 302 ± 12 μm; kcat = 14 min(-1)). Mass spectrometry analysis revealed that Scabin labels the exocyclic amino group on guanine bases in either single-stranded or double-stranded DNA. Several small molecule inhibitors were identified, and the most potent compounds were found to inhibit the enzyme activity with Ki values ranging from 3 to 24 μm PJ34, a well known inhibitor of poly-ADP-ribosyltransferases, was shown to be the most potent inhibitor of Scabin. Scabin was crystallized, representing the first structure of a DNA-targeting mono-ADP-ribosyltransferase enzyme; the structures of the apo-form (1.45 Å) and with two inhibitors (P6-E, 1.4 Å; PJ34, 1.6 Å) were solved. These x-ray structures are also the first high resolution structures of the Pierisin subgroup of the mono-ADP-ribosyltransferase toxin family. A model of Scabin with its DNA substrate is also proposed.
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Affiliation(s)
- Bronwyn Lyons
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada and
| | - Ravikiran Ravulapalli
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada and
| | - Jason Lanoue
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada and
| | - Miguel R Lugo
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada and
| | - Debajyoti Dutta
- the Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Stephanie Carlin
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada and
| | - A Rod Merrill
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada and
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Roth BM, Godoy-Ruiz R, Varney KM, Rustandi RR, Weber DJ. 1H, 13C, and 15N resonance assignments of an enzymatically active domain from the catalytic component (CDTa, residues 216-420) of a binary toxin from Clostridium difficile. BIOMOLECULAR NMR ASSIGNMENTS 2016; 10:213-217. [PMID: 26886352 PMCID: PMC4789081 DOI: 10.1007/s12104-016-9669-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 02/05/2016] [Indexed: 06/05/2023]
Abstract
Clostridium difficile is a bacterial pathogen and is the most commonly reported source of nosocomial infection in industrialized nations. Symptoms of C. difficile infection (CDI) include antibiotic-associated diarrhea, pseudomembranous colitis, sepsis and death. Over the last decade, rates and severity of hospital infections in North America and Europe have increased dramatically and correlate with the emergence of a hypervirulent strain of C. difficile characterized by the presence of a binary toxin, CDT (C. difficile toxin). The binary toxin consists of an enzymatic component (CDTa) and a cellular binding component (CDTb) that together form the active binary toxin complex. CDTa harbors a pair of structurally similar but functionally distinct domains, an N-terminal domain (residues 1-215; (1-215)CDTa) that interacts with CDTb and a C-terminal domain (residues 216-420; (216-420)CDTa) that harbors the intact ADP-ribosyltransferase (ART) active site. Reported here are the (1)H, (13)C, and (15)N backbone resonance assignments of the 23 kDa, 205 amino acid C-terminal enzymatic domain of CDTa, termed (216-420)CDTa. These NMR resonance assignments for (216-420)CDTa represent the first for a family of ART binary toxins and provide the framework for detailed characterization of the solution-state protein structure determination, dynamic studies of this domain, as well as NMR-based drug discovery efforts.
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Affiliation(s)
- Braden M Roth
- Center for Biomolecular Therapeutics (CBT), Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene St., Baltimore, MD, 21201, USA
| | - Raquel Godoy-Ruiz
- Center for Biomolecular Therapeutics (CBT), Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene St., Baltimore, MD, 21201, USA
| | - Kristen M Varney
- Center for Biomolecular Therapeutics (CBT), Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene St., Baltimore, MD, 21201, USA
| | - Richard R Rustandi
- Department of Vaccine Analytical Development, Merck Research Laboratories, 770 Sumneytown Pike, West Point, PA, 19486, USA
| | - David J Weber
- Center for Biomolecular Therapeutics (CBT), Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene St., Baltimore, MD, 21201, USA.
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